Well you tend to be throwing around the argument that this magical fourth slot is all clefable needs to succeed, but doesn't this kind of sound like 4mss? You want t-wave to be able to touch 80% of your counters (see mmeta, gengar, etc), you want knock off just to be annoying in general, you want CM to boost, you need moonblast/healing no matter what, you want ice beam to hit gliscor, you want tbolt/hp rock to beat talon, you want stored power to break past heatran and hit poisons, you want flamethrower to hit steels in general, you want focus blast to nail other steels, AND EVEN AFTER ALL THIS, pokemon like tentacruel, mega venusaur, and jirachi are still pretty much hard counters, and I'm sure i'm missing a few.
It's kinda like infernape. Nape has gunk shot for altaria/azu, thunderpunch for gyarados, stone edge for char-x/talon, gknot for rhyperior/quagsire, hp ice for garchomp/lando-t, mach punch to have priority, swords dance/nasty plot to break walls, etc. And even after all of that, lati@s are still pretty much flawless counters. Does it have the potential to annoy its checks? yes. Can it do it all at once? No. Are its moveslots matchup-based+require team support? yes. A lot like clefable.
and yeah, clefable's pretty annoying with its t-wave bs and such, but as long as you let one pokemon get paralyzed it often ends there; it's not exactly spreading para when i can just keep switching my tenta/heatran/ferro/etc in repeatedly to absorb thunder waves.
You also mentoin that clefable does well against diancie, lopuny, and mega altaria.
what?
252+ SpA Pixilate Mega Altaria Hyper Voice vs. 252 HP / 0 SpD Clefable: 204-241 (51.7 - 61.1%) -- 96.1% chance to 2HKO after Leftovers recovery
+1 192+ Atk Pixilate Mega Altaria Return vs. 252 HP / 252+ Def Clefable: 267-315 (67.7 - 79.9%) -- guaranteed 2HKO after Leftovers recovery
192+ Atk Pixilate Mega Altaria Return vs. 252 HP / 252+ Def Clefable: 178-210 (45.1 - 53.2%) -- 0.4% chance to 2HKO after Leftovers recovery
252 SpA Mega Diancie Moonblast vs. 252 HP / 4 SpD Clefable: 198-234 (50.2 - 59.3%) -- 79.3% chance to 2HKO after Leftovers recovery
252 Atk Mega Lopunny Return vs. 252 HP / 160 Def Clefable: 184-217 (46.7 - 55%) -- 14.1% chance to 2HKO after Leftovers recovery
252 Atk Mega Lopunny Return vs. 252 HP / 252+ Def Clefable: 153-180 (38.8 - 45.6%) -- guaranteed 3HKO after Leftovers recovery
Not only does clefable lose to every one of these with only about 10%-15% prior damage, each of these guys have ways of beating it even at full health.
Mega altaria sets up a dd as clefable switches in, and gets 2hko'd as it fails to OHKO with moonblast. T-wave can be dealt with via heal bell or refresh. Hyper voice cleanly 2hko's physically defensive variants.
Mega Diancie can set up a Cm as it switches in and 2hko with moonblast safely in every situation, and it often doesn't even need that. (yeah your beloved 4th moveslot doesn't do shit here)
Mega Lopunny is a little tricker, but if you're MG it can come in on a soft-boiled, encore you into it, power-up punch, and eventually 2hko with following returns. It can't even counter that.
This is what i mean; if its stats were higher then maybe it'd be able to take these attacks better and wouldn't need to left in fucking pristine shape to do anything.
MG maybe able to "outlast" its checks (of which there are often several), but its very easy to pressure and overwhelm. Unaware may be able to take on boosting mons better, but its far easier to wear down, and its recovery blows. Clefable cannot be both a great blanket check and difficult to wear down.
The 4th moveslot makes clefable annoying. But that's it. Not metagame defining. Not threatening. Not teambuilding-altering. Not S-rank worthy. Just annoying.